Hyper-V Replication and Differencing Disks

I fixed my issue by disabling the backup jobs for this server and then increased the replication frequency to 30 sec and gave it a few hours. Once the disks were merged completely then I enabled my backups again and they all works without any issue.

https://community.spiceworks.com/topic/1993546-hyper-v-checkpoint-merge-issues-2012-r2?page=1#entry-...